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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.


Current Build 155

Released April 9, 2021

Homo sapiens
chrX:125181298 (GRCh38.p13) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

T>A / T>C / T>G
Variation Type
SNV Single Nucleotide Variation
T=0.489796 (129644/264690, TOPMED)
T=0.48300 (15373/31828, ALFA)
C=0.49692 (6382/12843, 8.3KJPN) (+ 10 more)
C=0.4909 (1853/3775, 1000G)
T=0.4563 (1692/3708, TWINSUK)
C=0.4823 (1413/2930, KOREAN)
T=0.4486 (1296/2889, ALSPAC)
C=0.4739 (890/1878, HapMap)
T=0.147 (44/300, SGDP_PRJ)
C=0.426 (46/108, Qatari)
T=0.44 (21/48, Vietnamese)
T=0.42 (17/40, GENOME_DK)
T=0.21 (6/28, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TENM1 : Intron Variant
0 citations
Genomic View
See rs on genome

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p13 chr X NC_000023.11:g.125181298T>A
GRCh38.p13 chr X NC_000023.11:g.125181298T>C
GRCh38.p13 chr X NC_000023.11:g.125181298T>G
GRCh37.p13 chr X NC_000023.10:g.124315147T>A
GRCh37.p13 chr X NC_000023.10:g.124315147T>C
GRCh37.p13 chr X NC_000023.10:g.124315147T>G
Gene: TENM1, teneurin transmembrane protein 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TENM1 transcript variant 1 NM_001163278.1:c. N/A Genic Upstream Transcript Variant
TENM1 transcript variant 2 NM_001163279.1:c. N/A Genic Upstream Transcript Variant
TENM1 transcript variant 3 NM_014253.3:c. N/A Genic Upstream Transcript Variant
TENM1 transcript variant X7 XM_011531230.3:c.-65+3410…


N/A Intron Variant
TENM1 transcript variant X1 XM_017029208.2:c.-65+3410…


N/A Intron Variant
TENM1 transcript variant X2 XM_017029209.2:c.-120+341…


N/A Intron Variant
TENM1 transcript variant X3 XM_017029210.2:c.-65+4345…


N/A Intron Variant
TENM1 transcript variant X4 XM_017029211.2:c.-146+434…


N/A Intron Variant
TENM1 transcript variant X5 XM_017029212.2:c.-65+3410…


N/A Intron Variant
TENM1 transcript variant X6 XM_017029213.2:c.-65+4345…


N/A Intron Variant
TENM1 transcript variant X8 XM_017029214.2:c.-65+3410…


N/A Intron Variant
TENM1 transcript variant X11 XM_017029215.2:c.-65+3410…


N/A Intron Variant
TENM1 transcript variant X12 XM_017029216.2:c.-65+3410…


N/A Intron Variant
TENM1 transcript variant X9 XM_011531236.3:c. N/A Genic Upstream Transcript Variant
TENM1 transcript variant X10 XM_011531237.3:c. N/A Genic Upstream Transcript Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 31828 T=0.48300 A=0.00000, C=0.51700
European Sub 25534 T=0.47732 A=0.00000, C=0.52268
African Sub 3475 T=0.5652 A=0.0000, C=0.4348
African Others Sub 128 T=0.680 A=0.000, C=0.320
African American Sub 3347 T=0.5608 A=0.0000, C=0.4392
Asian Sub 176 T=0.523 A=0.000, C=0.477
East Asian Sub 116 T=0.552 A=0.000, C=0.448
Other Asian Sub 60 T=0.47 A=0.00, C=0.53
Latin American 1 Sub 232 T=0.496 A=0.000, C=0.504
Latin American 2 Sub 838 T=0.363 A=0.000, C=0.637
South Asian Sub 126 T=0.468 A=0.000, C=0.532
Other Sub 1447 T=0.4499 A=0.0000, C=0.5501


Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 T=0.489796 C=0.510204
8.3KJPN JAPANESE Study-wide 12843 T=0.50308 C=0.49692
1000Genomes Global Study-wide 3775 T=0.5091 C=0.4909
1000Genomes African Sub 1003 T=0.5414 C=0.4586
1000Genomes Europe Sub 766 T=0.517 C=0.483
1000Genomes East Asian Sub 764 T=0.555 C=0.445
1000Genomes South Asian Sub 718 T=0.510 C=0.490
1000Genomes American Sub 524 T=0.368 C=0.632
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.4563 C=0.5437
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.5177 C=0.4823, G=0.0000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 2889 T=0.4486 C=0.5514
HapMap Global Study-wide 1878 T=0.5261 C=0.4739
HapMap American Sub 768 T=0.474 C=0.526
HapMap African Sub 684 T=0.586 C=0.414
HapMap Asian Sub 254 T=0.516 C=0.484
HapMap Europe Sub 172 T=0.535 C=0.465
SGDP_PRJ Global Study-wide 300 T=0.147 C=0.853
Qatari Global Study-wide 108 T=0.574 C=0.426
A Vietnamese Genetic Variation Database Global Study-wide 48 T=0.44 C=0.56
The Danish reference pan genome Danish Study-wide 40 T=0.42 C=0.57
Siberian Global Study-wide 28 T=0.21 C=0.79

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement T= A C G
GRCh38.p13 chr X NC_000023.11:g.125181298= NC_000023.11:g.125181298T>A NC_000023.11:g.125181298T>C NC_000023.11:g.125181298T>G
GRCh37.p13 chr X NC_000023.10:g.124315147= NC_000023.10:g.124315147T>A NC_000023.10:g.124315147T>C NC_000023.10:g.124315147T>G
TENM1 transcript variant X7 XM_011531230.3:c.-65+3410= XM_011531230.3:c.-65+3410A>T XM_011531230.3:c.-65+3410A>G XM_011531230.3:c.-65+3410A>C
TENM1 transcript variant X1 XM_017029208.2:c.-65+3410= XM_017029208.2:c.-65+3410A>T XM_017029208.2:c.-65+3410A>G XM_017029208.2:c.-65+3410A>C
TENM1 transcript variant X2 XM_017029209.2:c.-120+3410= XM_017029209.2:c.-120+3410A>T XM_017029209.2:c.-120+3410A>G XM_017029209.2:c.-120+3410A>C
TENM1 transcript variant X3 XM_017029210.2:c.-65+4345= XM_017029210.2:c.-65+4345A>T XM_017029210.2:c.-65+4345A>G XM_017029210.2:c.-65+4345A>C
TENM1 transcript variant X4 XM_017029211.2:c.-146+4345= XM_017029211.2:c.-146+4345A>T XM_017029211.2:c.-146+4345A>G XM_017029211.2:c.-146+4345A>C
TENM1 transcript variant X5 XM_017029212.2:c.-65+3410= XM_017029212.2:c.-65+3410A>T XM_017029212.2:c.-65+3410A>G XM_017029212.2:c.-65+3410A>C
TENM1 transcript variant X6 XM_017029213.2:c.-65+4345= XM_017029213.2:c.-65+4345A>T XM_017029213.2:c.-65+4345A>G XM_017029213.2:c.-65+4345A>C
TENM1 transcript variant X8 XM_017029214.2:c.-65+3410= XM_017029214.2:c.-65+3410A>T XM_017029214.2:c.-65+3410A>G XM_017029214.2:c.-65+3410A>C
TENM1 transcript variant X11 XM_017029215.2:c.-65+3410= XM_017029215.2:c.-65+3410A>T XM_017029215.2:c.-65+3410A>G XM_017029215.2:c.-65+3410A>C
TENM1 transcript variant X12 XM_017029216.2:c.-65+3410= XM_017029216.2:c.-65+3410A>T XM_017029216.2:c.-65+3410A>G XM_017029216.2:c.-65+3410A>C

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

60 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss622 Sep 19, 2000 (36)
2 SC_SNP ss8185303 Apr 21, 2003 (114)
3 ABI ss43652676 Mar 13, 2006 (126)
4 AFFY ss76667715 Dec 08, 2007 (130)
5 HGSV ss85016418 Dec 15, 2007 (130)
6 BCMHGSC_JDW ss94392875 Mar 25, 2008 (129)
7 KRIBB_YJKIM ss104807685 Feb 05, 2009 (130)
8 1000GENOMES ss115138948 Jan 25, 2009 (130)
9 ENSEMBL ss133686606 Dec 01, 2009 (131)
10 ENSEMBL ss144806519 Dec 01, 2009 (131)
11 GMI ss157705611 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss163274513 Jul 04, 2010 (132)
13 COMPLETE_GENOMICS ss165595395 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss166518112 Jul 04, 2010 (132)
15 BUSHMAN ss204362776 Jul 04, 2010 (132)
16 BCM-HGSC-SUB ss208898160 Jul 04, 2010 (132)
17 GMI ss283862020 May 04, 2012 (137)
18 GMI ss287644302 Apr 25, 2013 (138)
19 PJP ss294503798 May 09, 2011 (134)
20 1000GENOMES ss341780747 May 09, 2011 (134)
21 ILLUMINA ss482733556 May 04, 2012 (137)
22 ILLUMINA ss484343048 May 04, 2012 (137)
23 ILLUMINA ss534758718 Sep 08, 2015 (146)
24 TISHKOFF ss567032452 Apr 25, 2013 (138)
25 ILLUMINA ss779133227 Aug 21, 2014 (142)
26 ILLUMINA ss781859583 Aug 21, 2014 (142)
27 ILLUMINA ss834597793 Aug 21, 2014 (142)
28 JMKIDD_LAB ss1083120183 Aug 21, 2014 (142)
29 DDI ss1432116005 Apr 01, 2015 (144)
30 1000GENOMES ss1556057600 Apr 01, 2015 (144)
31 EVA_GENOME_DK ss1583501558 Apr 01, 2015 (144)
32 EVA_UK10K_ALSPAC ss1641484944 Apr 01, 2015 (144)
33 EVA_UK10K_TWINSUK ss1684478977 Apr 01, 2015 (144)
34 WEILL_CORNELL_DGM ss1939701272 Feb 12, 2016 (147)
35 GENOMED ss1971431374 Jul 19, 2016 (147)
36 USC_VALOUEV ss2159229035 Dec 20, 2016 (150)
37 HUMAN_LONGEVITY ss2320160059 Dec 20, 2016 (150)
38 SYSTEMSBIOZJU ss2629771266 Nov 08, 2017 (151)
39 ILLUMINA ss2634984221 Nov 08, 2017 (151)
40 GRF ss2710346498 Nov 08, 2017 (151)
41 GNOMAD ss2983116265 Nov 08, 2017 (151)
42 SWEGEN ss3020583131 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3029114188 Nov 08, 2017 (151)
44 TOPMED ss3621355889 Nov 08, 2017 (151)
45 TOPMED ss3621355890 Nov 08, 2017 (151)
46 ILLUMINA ss3630480965 Oct 12, 2018 (152)
47 ILLUMINA ss3632868798 Oct 12, 2018 (152)
48 URBANLAB ss3651331857 Oct 12, 2018 (152)
49 EVA ss3770592094 Jul 14, 2019 (153)
50 PACBIO ss3788950067 Jul 14, 2019 (153)
51 PACBIO ss3793817741 Jul 14, 2019 (153)
52 PACBIO ss3798702743 Jul 14, 2019 (153)
53 KHV_HUMAN_GENOMES ss3823369730 Jul 14, 2019 (153)
54 EVA ss3836305984 Apr 27, 2020 (154)
55 EVA ss3841755021 Apr 27, 2020 (154)
56 EVA ss3847290075 Apr 27, 2020 (154)
57 SGDP_PRJ ss3892211726 Apr 27, 2020 (154)
58 KRGDB ss3942897282 Apr 27, 2020 (154)
59 TOPMED ss5136488364 Apr 26, 2021 (155)
60 TOMMO_GENOMICS ss5236165807 Apr 26, 2021 (155)
61 1000Genomes NC_000023.10 - 124315147 Oct 12, 2018 (152)
62 The Avon Longitudinal Study of Parents and Children NC_000023.10 - 124315147 Oct 12, 2018 (152)
63 The Danish reference pan genome NC_000023.10 - 124315147 Apr 27, 2020 (154)
64 HapMap NC_000023.11 - 125181298 Apr 27, 2020 (154)
65 KOREAN population from KRGDB NC_000023.10 - 124315147 Apr 27, 2020 (154)
66 Qatari NC_000023.10 - 124315147 Apr 27, 2020 (154)
67 SGDP_PRJ NC_000023.10 - 124315147 Apr 27, 2020 (154)
68 Siberian NC_000023.10 - 124315147 Apr 27, 2020 (154)
69 8.3KJPN NC_000023.10 - 124315147 Apr 26, 2021 (155)
70 TopMed NC_000023.11 - 125181298 Apr 26, 2021 (155)
71 UK 10K study - Twins NC_000023.10 - 124315147 Oct 12, 2018 (152)
72 A Vietnamese Genetic Variation Database NC_000023.10 - 124315147 Jul 14, 2019 (153)
73 ALFA NC_000023.11 - 125181298 Apr 26, 2021 (155)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID History Updated (Build)
rs6649754 Aug 27, 2003 (117)
rs56556643 May 25, 2008 (130)
rs59164500 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
9378229531, ss3621355889 NC_000023.11:125181297:T:A NC_000023.11:125181297:T:A (self)
ss85016418 NC_000023.8:124040681:T:C NC_000023.11:125181297:T:C (self)
ss94392875, ss115138948, ss163274513, ss165595395, ss166518112, ss204362776, ss208898160, ss283862020, ss287644302, ss294503798, ss484343048 NC_000023.9:124142827:T:C NC_000023.11:125181297:T:C (self)
84017001, 46282189, 9666495, 50074676, 21743194, 44228706, 11745389, 94135114, 46282189, 10174585, ss341780747, ss482733556, ss534758718, ss567032452, ss779133227, ss781859583, ss834597793, ss1083120183, ss1432116005, ss1556057600, ss1583501558, ss1641484944, ss1684478977, ss1939701272, ss1971431374, ss2159229035, ss2629771266, ss2634984221, ss2710346498, ss2983116265, ss3020583131, ss3630480965, ss3632868798, ss3770592094, ss3788950067, ss3793817741, ss3798702743, ss3836305984, ss3841755021, ss3892211726, ss3942897282, ss5236165807 NC_000023.10:124315146:T:C NC_000023.11:125181297:T:C (self)
4032806, 436756076, 700094721, 9378229531, ss2320160059, ss3029114188, ss3621355890, ss3651331857, ss3823369730, ss3847290075, ss5136488364 NC_000023.11:125181297:T:C NC_000023.11:125181297:T:C (self)
ss622, ss8185303, ss43652676, ss76667715, ss104807685, ss133686606, ss144806519, ss157705611 NT_011786.16:8582856:T:C NC_000023.11:125181297:T:C (self)
50074676, ss3942897282 NC_000023.10:124315146:T:G NC_000023.11:125181297:T:G (self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs617


The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post596+ae089ad